Transcriptomics

Training material for all kinds of transcriptomics analysis.

Requirements

Before diving into this topic, we recommend you to have a look at:

• Introduction to Galaxy Analyses
• Sequence analysis
  • Quality Control: slides slides - tutorial hands-on
  • Mapping: slides slides - tutorial hands-on

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/transcriptomics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Maintainers

This material is maintained by:

Bérénice Batut

Maria Doyle

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Bérénice Batut

Anika Erxleben

Markus Wolfien

Florian Heyl

Daniel Maticzka

Hans-Rudolf Hotz

Mehmet Tekman

Mallory Freeberg

Mo Heydarian

Alex Ostrovsky

IGC Bioinformatics Unit

Maria Doyle

Chao (Cico) Zhang

Wendi Bacon

Daniel Blankenberg

Wolfgang Maier

Pavankumar Videm

Clemens Blank

Nicola Soranzo

Peter van Heusden

Fotis E. Psomopoulos

Toby Hodges

Xavier Garnier

Anthony Bretaudeau

Anne Siegel

Olivier Dameron

Belinda Phipson

Jovana Maksimovic

Anna Trigos

Matt Ritchie

Harriet Dashnow

Shian Su

Charity Law

Graham Etherington

Andrea Bagnacani

References

• Shirley Pepke et al: Computation for ChIP-seq and RNA-seq studies
• Paul L. Auer & R. W. Doerge: Statistical Design and Analysis of RNA Sequencing Data
  Insights into proper planning of your RNA-seq run! To read before any RNA-seq experiment!
• Ian Korf: Genomics: the state of the art in RNA-seq analysis
  A refreshingly honest view on the non-trivial aspects of RNA-seq analysis
• Marie-Agnès Dillies et al: A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
  Systematic comparison of seven representative normalization methods for the differential analysis of RNA-seq data (Total Count, Upper Quartile, Median (Med), DESeq, edgeR, Quantile and Reads Per Kilobase per Million mapped reads (RPKM) normalization)
• Franck Rapaport et al: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
  Evaluation of methods for differential gene expression analysis
• Charlotte Soneson & Mauro Delorenzi: A comparison of methods for differential expression analysis of RNA-seq data
• Adam Roberts et al: Improving RNA-Seq expression estimates by correcting for fragment bias
• Manuel Garber et al: Computational methods for transcriptome annotation and quantification using RNA-seq
  Classical paper about the computational aspects of RNA-seq data analysis
• Cole Trapnell et al: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
• Zhong Wang et al: RNA-Seq: a revolutionary tool for transcriptomics
• Dittrich, M. T. and Klau, G. W. and Rosenwald, A. and Dandekar, T. and Muller, T.: Identifying functional modules in protein-protein interaction networks: an integrated exact approach
• May, Ali; Brandt, Bernd W; El-Kebir, Mohammed; Klau, Gunnar W; Zaura, Egija; Crielaard, Wim; Heringa, Jaap; Abeln, Sanne: metaModules identifies key functional subnetworks in microbiome-related disease
• Pavankumar, Videm; Dominic, Rose; Fabrizio, Costa; Rolf, Backofen: BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles